I will let you know about the stainless steel brake line improvements, I plan on installing some in the next month or two.
And yes, the Happy Trails rack looks pretty beefy, I may go with the full system, but may also investigate other aluminum box options as well. I can't go too wide with the boxes as the muffler sticks out of the right side. Happy Trails has boxes which should keep the distance even from the centerline of the bike to the outside of the panniers. This involves using different widths of boxes on each side.
Anyone upgraded the rear shock on their Transalp?